Genome wide association study and differential gene expression of Drosophila melanogaster under heat and cold stress
TS O’Leary
1 MA plots
All MA plots now have an FDR cutoff of 0.01 and no fold-change cutoff.
1.1 No gene labels
Cold v Ctrl MA plot
Hot v Ctrl MA plot
1.2 Labeled by padj
Cold v Ctrl MA plot
Hot v Ctrl MA plot
1.3 GWAS points
Cold v Ctrl MA plot
Hot v Ctrl MA plot
1.4 GWAS labels
Cold v Ctrl MA plot
Hot v Ctrl MA plot
1.5 GWAS labels colored by DEG sig
Cold v Ctrl MA plot
Hot v Ctrl MA plot
2 Top 50 differentially expressed genes
2.1 Heat shock
| gene | hot_fc | log2FoldChange.hot | padj.hot |
|---|---|---|---|
| CG3339 | down | -5.155 | 1.097e-27 |
| l(2)08717 | down | -2.3 | 4.051e-25 |
| pip | down | -3.434 | 5.188e-24 |
| stan | down | -2.592 | 2.063e-23 |
| Dhc36C | down | -2.724 | 1.51e-22 |
| ft | down | -3.361 | 4.602e-22 |
| CG17075 | down | -2.455 | 5.379e-22 |
| CG1801 | down | -3.692 | 2.458e-21 |
| CG9492 | down | -4.122 | 2.881e-20 |
| Dhc93AB | down | -3.104 | 1.029e-19 |
| Dscam1 | down | -1.795 | 1.792e-19 |
| CG42534 | down | -4.148 | 4.16e-19 |
| CG6125 | down | -2.153 | 7.197e-19 |
| CG1688 | down | -3.061 | 8.789e-19 |
| btv | down | -4.624 | 1.002e-18 |
| Sb | down | -4.59 | 1.126e-18 |
| CG43980 | down | -4.82 | 1.34e-18 |
| Muc14A | down | -2.612 | 1.372e-18 |
| hiw | down | -1.521 | 1.414e-18 |
| CG3348 | down | -3.219 | 1.822e-18 |
| Nos | down | -3.834 | 2.877e-18 |
| CG30263 | down | -3.978 | 4.212e-18 |
| jv | down | -2.334 | 4.212e-18 |
| conv | down | -4.136 | 4.94e-18 |
| NT1 | down | -6.652 | 4.94e-18 |
| Dop1R1 | down | -2.643 | 6.474e-18 |
| Shawl | down | -3.459 | 8.688e-18 |
| CG8745 | down | -2.145 | 1.314e-17 |
| CG14304 | down | -4.486 | 1.542e-17 |
| CG31465 | down | -6.373 | 2.078e-17 |
| Ugt86Di | down | -5.074 | 4.038e-17 |
| CR44327 | down | -2.536 | 4.654e-17 |
| salr | down | -3.028 | 4.671e-17 |
| nompC | down | -3.89 | 6.068e-17 |
| SIFaR | down | -4.022 | 6.357e-17 |
| Nlg4 | down | -2.488 | 8.891e-17 |
| CG15894 | down | -2.427 | 1.946e-16 |
| Cda5 | down | -1.12 | 2.097e-16 |
| CG4744 | down | -6.327 | 2.705e-16 |
| eag | down | -1.729 | 2.931e-16 |
| CG30272 | down | -3.39 | 3.009e-16 |
| Ac78C | down | -2.352 | 3.672e-16 |
| CG45105 | down | -3.336 | 4.007e-16 |
| Rab26 | down | -2.214 | 4.049e-16 |
| CG12950 | down | -2.918 | 4.628e-16 |
| CG32791 | down | -1.702 | 5.419e-16 |
| TkR99D | down | -3.825 | 8.6e-16 |
| Ddr | down | -3.329 | 9.219e-16 |
| GABA-B-R1 | down | -2.256 | 1.09e-15 |
| Sytbeta | down | -3.292 | 1.449e-15 |
| Hsp68 | up | 6.888 | 0 |
| DnaJ-1 | up | 3.727 | 2.219e-143 |
| Hsp70Bb | up | 7.003 | 2.219e-143 |
| stv | up | 4.471 | 2.373e-104 |
| Hsp26 | up | 4.279 | 5.676e-72 |
| Hsp67Bc | up | 4.785 | 2.957e-71 |
| Hsp27 | up | 3.532 | 4.06e-62 |
| Hsp83 | up | 2.106 | 6.281e-58 |
| Hsp23 | up | 6.872 | 8.789e-53 |
| Nop17l | up | 1.614 | 7.563e-52 |
| CG6770 | up | 1.78 | 5.402e-48 |
| Hop | up | 1.305 | 1.268e-43 |
| CG42240 | up | 1.131 | 1.65e-41 |
| Hsc70Cb | up | 1.271 | 5.313e-38 |
| Jafrac1 | up | 0.8308 | 7.251e-38 |
| CG16721 | up | 1.484 | 1.699e-36 |
| CG1416 | up | 1.24 | 1.833e-34 |
| CG5290 | up | 1.882 | 8.359e-34 |
| Droj2 | up | 1.165 | 9.102e-33 |
| Hsc70-3 | up | 1.522 | 2.984e-32 |
| Lsd-2 | up | 1.004 | 2.845e-30 |
| alphagamma-element:CR32865 | up | 6.317 | 1.507e-29 |
| sra | up | 1.258 | 9.836e-29 |
| CG10600 | up | 1.189 | 1.267e-28 |
| Mlf | up | 1.019 | 1.689e-28 |
| Capr | up | 0.9256 | 6.875e-28 |
| mim | up | 1.18 | 1.125e-26 |
| Hsp70Bc | up | 5.778 | 5.299e-26 |
| CG10077 | up | 1.398 | 5.714e-26 |
| Pgi | up | 0.9688 | 3e-25 |
| ref(2)P | up | 1.398 | 7.851e-24 |
| CG7033 | up | 1.009 | 4.144e-23 |
| e(y)3 | up | 0.9014 | 8.199e-23 |
| Trxr-1 | up | 1.139 | 1.335e-22 |
| Pa1 | up | 1.987 | 1.445e-22 |
| CG1943 | up | 1.14 | 1.445e-22 |
| PEK | up | 1.254 | 5.637e-22 |
| GstD1 | up | 0.8593 | 7.088e-22 |
| phol | up | 1.028 | 8.707e-22 |
| CG3680 | up | 0.8435 | 4.633e-21 |
| TfIIEalpha | up | 1.076 | 1.121e-20 |
| da | up | 0.8578 | 2.725e-20 |
| cact | up | 0.8173 | 3.294e-20 |
| Ran | up | 0.7748 | 6.905e-20 |
| CG1677 | up | 0.8251 | 9.427e-20 |
| betaTub56D | up | 1.038 | 1.749e-19 |
| Cctgamma | up | 0.8277 | 6.345e-19 |
| BRWD3 | up | 0.8852 | 7.197e-19 |
| l(1)G0469 | up | 1.272 | 7.197e-19 |
| Pdk | up | 1.35 | 1.224e-18 |
2.2 Cold shock
| gene | cold_fc | log2FoldChange.cold | padj.cold |
|---|---|---|---|
| stan | down | -2.535 | 2.296e-20 |
| Dhc93AB | down | -3.204 | 2.253e-19 |
| CG3339 | down | -4.294 | 5.99e-19 |
| CG1801 | down | -3.666 | 5.99e-19 |
| CG3280 | down | -3.068 | 5.99e-19 |
| CG42534 | down | -4.469 | 7.335e-19 |
| CG32791 | down | -1.855 | 1.687e-17 |
| ft | down | -2.987 | 8.646e-17 |
| pip | down | -2.89 | 1.435e-16 |
| Dscam1 | down | -1.683 | 2.136e-16 |
| CG43163 | down | -3.52 | 4.912e-16 |
| CG9492 | down | -3.725 | 5.06e-16 |
| rk | down | -3.238 | 8.245e-16 |
| Dhc36C | down | -2.296 | 1.463e-15 |
| CG8219 | down | -5.491 | 1.463e-15 |
| SIFaR | down | -4.039 | 2.331e-15 |
| Ac78C | down | -2.361 | 3.608e-15 |
| Ddr | down | -3.388 | 6.724e-15 |
| d | down | -3.775 | 1.027e-14 |
| CR45604 | down | -3.018 | 1.027e-14 |
| mtt | down | -3.664 | 1.135e-14 |
| Dhc62B | down | -3.892 | 1.49e-14 |
| iav | down | -4.075 | 1.696e-14 |
| CR45272 | down | -4.647 | 2.839e-14 |
| prom | down | -2.737 | 2.839e-14 |
| CG18519 | down | -3.233 | 2.839e-14 |
| CG43110 | down | -3.216 | 4.113e-14 |
| Nep5 | down | -3.804 | 4.113e-14 |
| conv | down | -3.69 | 6.626e-14 |
| rdgC | down | -1.94 | 6.946e-14 |
| Shawl | down | -3.097 | 7.672e-14 |
| CG44153 | down | -3.691 | 8.047e-14 |
| Hsp68 | down | -1.071 | 8.344e-14 |
| GluRIB | down | -2.415 | 9.254e-14 |
| CG45002 | down | -1.938 | 9.254e-14 |
| Sb | down | -3.89 | 1.557e-13 |
| Nlg4 | down | -2.28 | 1.557e-13 |
| CG4744 | down | -5.989 | 1.789e-13 |
| trh | down | -2.138 | 2.011e-13 |
| btv | down | -3.901 | 2.345e-13 |
| rdo | down | -3.167 | 2.827e-13 |
| Dop1R1 | down | -2.284 | 4.304e-13 |
| unc-13-4A | down | -2.109 | 4.464e-13 |
| TrpA1 | down | -4.111 | 4.79e-13 |
| CG42255 | down | -1.631 | 5.093e-13 |
| CG31814 | down | -3.185 | 5.781e-13 |
| rad | down | -1.922 | 6.059e-13 |
| Muc68Ca | down | -3.064 | 6.059e-13 |
| CG43795 | down | -2.427 | 6.591e-13 |
| eag | down | -1.562 | 7.105e-13 |
| Jafrac1 | up | 0.6228 | 1.102e-19 |
| Lsd-2 | up | 0.8045 | 1.486e-18 |
| endos | up | 0.7605 | 1.544e-17 |
| D1 | up | 0.684 | 1.687e-17 |
| Muc4B | up | 2.542 | 1.687e-17 |
| Capr | up | 0.7236 | 2.497e-16 |
| CG14478 | up | 0.8465 | 3.717e-15 |
| CG1677 | up | 0.73 | 7.404e-15 |
| Ran | up | 0.6814 | 7.51e-15 |
| CG15771 | up | 0.6845 | 1.537e-14 |
| bif | up | 0.7919 | 2.869e-14 |
| GstD1 | up | 0.7024 | 3.842e-14 |
| e(y)3 | up | 0.7182 | 4.174e-14 |
| mts | up | 0.638 | 6.428e-14 |
| phol | up | 0.8291 | 9.254e-14 |
| east | up | 0.7952 | 1.511e-13 |
| Act5C | up | 0.6184 | 2.345e-13 |
| CG8223 | up | 0.9441 | 2.752e-13 |
| cact | up | 0.6657 | 4.446e-13 |
| Rip11 | up | 0.7142 | 5.651e-13 |
| CG1440 | up | 0.6414 | 5.951e-13 |
| ssx | up | 0.6681 | 7.105e-13 |
| swa | up | 0.8273 | 1.017e-12 |
| tral | up | 0.8757 | 1.203e-12 |
| CG1943 | up | 0.8542 | 1.883e-12 |
| Pen | up | 0.898 | 2.887e-12 |
| cib | up | 0.8765 | 3.891e-12 |
| nocte | up | 0.7272 | 5.576e-12 |
| CG6597 | up | 0.6554 | 5.593e-12 |
| CG8963 | up | 0.6505 | 5.707e-12 |
| mim | up | 0.7948 | 6.11e-12 |
| Hmt4-20 | up | 0.7751 | 6.589e-12 |
| CG12262 | up | 0.8364 | 1.29e-11 |
| 26-29-p | up | 0.8999 | 1.457e-11 |
| rngo | up | 0.6756 | 1.476e-11 |
| Jupiter | up | 0.6516 | 1.526e-11 |
| CG4511 | up | 0.7374 | 1.68e-11 |
| da | up | 0.6498 | 1.814e-11 |
| pr-set7 | up | 0.8255 | 2.345e-11 |
| Cap | up | 0.775 | 2.683e-11 |
| CG10492 | up | 0.844 | 2.975e-11 |
| Gapdh2 | up | 0.7177 | 3.343e-11 |
| Rpt1 | up | 0.5432 | 3.942e-11 |
| Df31 | up | 0.7823 | 4.048e-11 |
| CG8108 | up | 0.6396 | 4.688e-11 |
| betaTub56D | up | 0.7807 | 5.6e-11 |
| Upf1 | up | 0.6236 | 5.655e-11 |
| CG9705 | up | 0.7375 | 8.723e-11 |
| Abi | up | 0.6488 | 8.733e-11 |
| Amun | up | 0.7009 | 9.284e-11 |
3 DEG LFC scatter & GWAS Density
3.1 GWAS scatter & density plots (10^-5)
| GWAS distributions | Heat-shock | Cold-shock |
|---|---|---|
| Other vs. CTmin | 0.5641033 | 0.5775028 |
| Other vs. CTmax | 0.4426838 | 0.6970872 |
| CTmin vs. CTmax | 0.5715501 | 0.8135801 |
3.2 GWAS scatter & density plots (10^-4)
| GWAS distributions | Heat-shock | Cold-shock |
|---|---|---|
| Other vs. CTmin | 0.1475051 | 0.0679122 |
| Other vs. CTmax | 0.0054554 | 0.0091421 |
| Other vs. Both | 0.9848098 | 0.9328658 |
| CTmin vs. CTmax | 0.1531904 | 0.0452680 |
| CTmin vs. Both | 0.9781510 | 0.9716340 |
| CTmax vs. Both | 0.8753813 | 0.9695981 |
3.3 GWAS scatter & density plots (10^-4) rm both
| GWAS distributions | Heat-shock | Cold-shock |
|---|---|---|
| Other vs. CTmin | 0.1475051 | 0.0679122 |
| Other vs. CTmax | 0.0054554 | 0.0091421 |
| CTmin vs. CTmax | 0.1531904 | 0.0452680 |
4 DEG LFC scatter
4.1 No labels
4.2 GWAS hits labeled
4.3 With unique labeled
4.4 With shared labeled
4.5 With shared labeled (padj.hot)
5 GWAS Tables
5.1 GWAS summary table
| GWAS | SNPs | SNPs annotated to genes | Unique genes | Sig DEGs | NS DEGs | No RNAseq data |
|---|---|---|---|---|---|---|
| CTmax | 21 | 19 | 12 | 9 | 3 | 0 |
| CTmin | 53 | 50 | 26 | 11 | 12 | 3 |
5.2 CTmax
5.2.1 All hits (pval cutoff 10^-5)
| ID | gene | grps | AvgMixedPval |
|---|---|---|---|
| 2R_10330800_INS | Oaz | INTRON | 8.0e-07 |
| 2R_6398772_SNP | lola | INTRON | 9.0e-07 |
| 2R_6398743_SNP | lola | INTRON | 9.0e-07 |
| 2R_10330805_SNP | Oaz | INTRON | 1.0e-06 |
| 3R_22515826_SNP | 2.3e-06 | ||
| 2L_12384183_SNP | bru-2 | INTRON | 2.4e-06 |
| 3R_25373467_SNP | 2.5e-06 | ||
| 2R_17564376_SNP | CG30263 | SYNONYMOUS_CODING | 2.6e-06 |
| 2R_10330722_SNP | Oaz | INTRON | 3.0e-06 |
| X_3381582_SNP | CR44999 | INTRON | 3.2e-06 |
| X_3381582_SNP | CG10803 | INTRON | 3.2e-06 |
| X_3381590_SNP | CG10803 | INTRON | 3.2e-06 |
| X_3381590_SNP | CR44999 | INTRON | 3.2e-06 |
| 2R_10330717_SNP | Oaz | INTRON | 3.5e-06 |
| X_3381391_SNP | CR44999 | INTRON | 3.7e-06 |
| X_3381391_SNP | CG10803 | INTRON | 3.7e-06 |
| X_3381587_SNP | CR44999 | INTRON | 4.1e-06 |
| X_3381587_SNP | CG10803 | INTRON | 4.1e-06 |
| 3L_9575326_SNP | CG42673 | INTRON | 6.0e-06 |
| X_5876026_SNP | Grip | INTRON | 6.0e-06 |
| 3R_3427376_SNP | CG34127 | INTRON | 7.6e-06 |
| 2L_19428598_SNP | CG13085 | INTRON | 8.4e-06 |
| 2L_19428598_SNP | CG16771 | INTRON | 8.4e-06 |
| 2R_10330701_SNP | Oaz | INTRON | 9.7e-06 |
| 2L_19428336_SNP | CG13085 | INTRON | 9.9e-06 |
| 2L_19428336_SNP | CG16771 | INTRON | 9.9e-06 |
| 3R_20025347_SNP | twin | INTRON | 1.0e-05 |
5.2.2 Group count
| grps | n |
|---|---|
| INTRON | 24 |
| SYNONYMOUS_CODING | 1 |
5.2.3 Gene counts
| gene | n |
|---|---|
| Oaz | 5 |
| CG10803 | 4 |
| CR44999 | 4 |
| CG13085 | 2 |
| CG16771 | 2 |
| lola | 2 |
| bru-2 | 1 |
| CG30263 | 1 |
| CG34127 | 1 |
| CG42673 | 1 |
| Grip | 1 |
| twin | 1 |
5.3 CTmin
5.3.1 All hits (pval cutoff 10^-5)
| ID | gene | grps | AvgMixedPval |
|---|---|---|---|
| 2R_20313579_SNP | prom | INTRON | 0.0e+00 |
| 2R_20313579_SNP | CG42383 | INTRON | 0.0e+00 |
| X_4385442_SNP | CR32773 | INTRON | 1.0e-07 |
| 3R_13900959_SNP | 2.0e-07 | ||
| 2R_20308502_SNP | prom | INTRON | 4.0e-07 |
| 3R_12992895_SNP | Mur89F | INTRON | 7.0e-07 |
| 2R_20313917_SNP | prom | INTRON | 9.0e-07 |
| 2R_20313922_DEL | prom | INTRON | 9.0e-07 |
| 2R_20313930_SNP | prom | INTRON | 9.0e-07 |
| 2R_20313933_SNP | prom | INTRON | 9.0e-07 |
| 2R_20313935_INS | prom | INTRON | 9.0e-07 |
| 2R_20313938_SNP | prom | INTRON | 9.0e-07 |
| 2R_20313940_MNP | prom | INTRON | 9.0e-07 |
| 2R_20308558_SNP | prom | INTRON | 1.0e-06 |
| 2R_20250118_SNP | bs | INTRON | 1.0e-06 |
| 2R_20250118_SNP | CR44811 | INTRON | 1.0e-06 |
| 2R_20301097_SNP | CG45068 | SYNONYMOUS_CODING | 1.1e-06 |
| 2R_20301097_SNP | CG45069 | SYNONYMOUS_CODING | 1.1e-06 |
| 2R_20301239_SNP | CG45068 | NON_SYNONYMOUS_CODING | 1.1e-06 |
| 2R_20301239_SNP | CG45069 | NON_SYNONYMOUS_CODING | 1.1e-06 |
| 2R_20308533_SNP | prom | INTRON | 1.2e-06 |
| 2R_20313914_SNP | prom | INTRON | 1.3e-06 |
| 2L_2612712_SNP | 1.4e-06 | ||
| 2R_20313927_SNP | prom | INTRON | 1.5e-06 |
| 2R_20313911_SNP | prom | INTRON | 1.8e-06 |
| 2R_20307893_SNP | prom | NON_SYNONYMOUS_CODING | 1.8e-06 |
| 2R_20313916_SNP | prom | INTRON | 1.9e-06 |
| 2R_20308565_SNP | prom | INTRON | 1.9e-06 |
| 2R_20309964_SNP | prom | INTRON | 2.0e-06 |
| 2R_20309106_SNP | prom | INTRON | 2.2e-06 |
| 3R_11364111_SNP | CG18519 | SYNONYMOUS_CODING | 2.2e-06 |
| 2R_20313919_SNP | prom | INTRON | 2.4e-06 |
| 3R_14850882_SNP | CG14285 | NON_SYNONYMOUS_CODING | 3.1e-06 |
| 3R_14850882_SNP | CG14286 | NON_SYNONYMOUS_CODING | 3.1e-06 |
| 2R_20313912_SNP | prom | INTRON | 3.2e-06 |
| 2L_3465546_SNP | msl-2 | NON_SYNONYMOUS_CODING | 3.2e-06 |
| 2L_3465546_SNP | Pdsw | NON_SYNONYMOUS_CODING | 3.2e-06 |
| 2R_20301123_SNP | CG45069 | UTR_5_PRIME | 3.3e-06 |
| 2R_20301123_SNP | CG45068 | UTR_5_PRIME | 3.3e-06 |
| 3R_13552400_SNP | Lgr1 | INTRON | 3.6e-06 |
| 3R_11367299_SNP | CG18519 | NON_SYNONYMOUS_CODING | 4.0e-06 |
| 3R_11288771_SNP | AdamTS-A | INTRON | 4.2e-06 |
| 2R_20301091_SNP | CG45069 | UTR_5_PRIME | 4.2e-06 |
| 2R_20301091_SNP | CG45068 | UTR_5_PRIME | 4.2e-06 |
| 2R_12301745_SNP | Sema-2b | INTRON | 4.2e-06 |
| 2R_12301745_SNP | Menl-2 | INTRON | 4.2e-06 |
| 3R_12990694_SNP | Mur89F | INTRON | 4.3e-06 |
| 2R_20309307_SNP | prom | INTRON | 4.8e-06 |
| 3R_9949217_SNP | twf | SYNONYMOUS_CODING | 5.6e-06 |
| 3R_9949217_SNP | 140up | SYNONYMOUS_CODING | 5.6e-06 |
| 3R_13002842_SNP | Mur89F | INTRON | 5.7e-06 |
| 2R_20309122_SNP | prom | INTRON | 5.8e-06 |
| 3R_12997215_SNP | Mur89F | INTRON | 6.0e-06 |
| 2L_3396579_SNP | CR44792 | DOWNSTREAM | 6.6e-06 |
| 2L_3396577_SNP | CR44792 | DOWNSTREAM | 6.7e-06 |
| 3R_13552010_SNP | Lgr1 | INTRON | 6.7e-06 |
| 3L_4694662_SNP | CG15876 | SYNONYMOUS_CODING | 7.5e-06 |
| 3L_4694662_SNP | RhoGEF64C | SYNONYMOUS_CODING | 7.5e-06 |
| X_5639729_SNP | IntS6 | INTRON | 7.5e-06 |
| 2L_2612282_INS | CG15395 | DOWNSTREAM | 7.6e-06 |
| 2R_7024700_SNP | BBS4 | SYNONYMOUS_CODING | 7.8e-06 |
| 2R_20313809_SNP | prom | INTRON | 9.0e-06 |
| 3L_5853164_SNP | 9.6e-06 | ||
| 2L_3885863_SNP | capu | INTRON | 9.7e-06 |
5.3.2 Group count
| grps | n |
|---|---|
| INTRON | 38 |
| NON_SYNONYMOUS_CODING | 8 |
| SYNONYMOUS_CODING | 8 |
| UTR_5_PRIME | 4 |
| DOWNSTREAM | 3 |
5.3.3 Gene counts
| gene | n |
|---|---|
| prom | 24 |
| CG45068 | 4 |
| CG45069 | 4 |
| Mur89F | 4 |
| CG18519 | 2 |
| CR44792 | 2 |
| Lgr1 | 2 |
| 140up | 1 |
| AdamTS-A | 1 |
| BBS4 | 1 |
| bs | 1 |
| capu | 1 |
| CG14285 | 1 |
| CG14286 | 1 |
| CG15395 | 1 |
| CG15876 | 1 |
| CG42383 | 1 |
| CR32773 | 1 |
| CR44811 | 1 |
| IntS6 | 1 |
| Menl-2 | 1 |
| msl-2 | 1 |
| Pdsw | 1 |
| RhoGEF64C | 1 |
| Sema-2b | 1 |
| twf | 1 |